CLOTHO is what I hear the most about, but it seems very buggy when I try to use it on my Mac, so I haven't been able to do anything with it.

TinkerCell has a neat interface and some simulation functions, but I don't think it is supported any more.

TeselaGen is a company with a Beta of a synthetic biology tool going on right now. You can register and play with it for free, I believe.

The iGEM team usually ends up using Geneious to design their constructs, but it doesn't have any real CAD functions except for editing sequences with annotations and drawing nice pictures.

Also, check out the software division of iGEM. It has a lot of "Best-X-tool" prizes, which must mean that X is a synthetic biology CAD framework.

Kevin Baldridge 14:33, 2 February 2013 (EST):Thanks, these are all great leads and better than most of what I was able to find with a quick google search. I'll flesh this out more today

Gabriel Wu 15:13, 4 February 2013 (EST): j5 is a program coming from Nathan Hillson at the Joint Bioenergy Institute at Berkeley (JBEI). It automatically designs oligonucleotides for gene assembly for Gibson and Gibson-like synthesis.

Gabriel Wu 16:56, 4 February 2013 (EST): I think for the Basic Features, things like VectorNTI (commercial), geneious, amplify (virtual PCR), and maybe even sequence aligners like BLAST might be considered CAD at this basic level.

Gabriel Wu 17:07, 4 February 2013 (EST): I don't think it belongs here, but there are lots of biological modeling projects going on these days. These systems are too complex to engineer de novo, but I think understanding these things or trying to will aid in engineering simpler systems. Maybe this belongs more in a future directions section. Here's fun list

Gabriel Wu: Oh, how about flux balance analysis (FBA)? Does this have a role here at all?

Gabriel Wu 17:26, 4 February 2013 (EST): What are the killer apps for synthetic biology?